The concept of “metabolic inflexibility” was first introduced to describe the failure of insulin resistant human subjects to appropriately adjust mitochondrial fuel selection in response to nutritional cues. This phenomenon has since gained increasing recognition as a core component of the metabolic syndrome, but its molecular basis has remained elusive. Recent work in our laboratory suggests that metabolic inflexibility in the obese state might be partly attributable to a decline in muscle activity of carnitine acetyltransferase (CrAT), a mitochondrial matrix enzyme that catalyzes the conversion of acetyl-CoA and other short chain acyl-CoAs to their membrane permeant acylcarnitine esters. By doing so, CrAT regulates intracellular and inter-tissue trafficking of carbon intermediates. Studies in muscle-specific Crat knockout mice, primary human skeletal myocytes and human subjects undergoing L-carnitine supplementation revealed an essential role for CrAT in controlling substrate switching, glucose tolerance and exercise performance. The results support a model wherein CrAT promotes metabolic flexibility during feeding and exercise by permitting mitochondrial efflux of excess acetyl moieties that otherwise inhibit key regulatory enzymes, such as pyruvate dehydrogenase. These findings along with ongoing studies seeking to further delineate the role of CrAT in combatting nutrient-induced mitochondrial stress will be discussed.